tbuckley/cabot-search huggingface dataset:
Abstract LB528: A microglia associated gene signature predicts survival risk in glioma patients
Authors: Chongming Jiang, Evelien Schaafsma, Yanding Zhao, Thinh Nguyen, Kenneth Zhu, Chao Cheng
Journal: Cancer Research (2022)

Abstract Background: Gliomas are common tumors that affect the brain and spinal cord. A complex tumor microenvironment is one of the leading reasons for a poor prognosis in glioma patients. Microglia, as part of the immune microenvironment of gliomas, may facilitate glioma growth and invasion. However, the correlation between the microglia abundance and glioma prognosis has not been clarified. Method: Our goal was to examine the relationship between microglia abundance and glioma prognosis. We analyzed the single-cell RNA sequences of human and mouse glioma cells to identify microglia marker genes. Then, we built a LASSO Cox regression model of microglia abundance signatures in gliomas. The Cancer Genome Atlas (TCGA) dataset (Low-grade gliomas, LGG) was used as the training cohort. The Repository of Molecular Brain Neoplasia Data (REMBRANDT) dataset and Chinese Glioma Genome Atlas (CGGA) dataset was used to validate the model as the validation cohorts. Findings: Overall survival was significantly lower in those with a high level of microglia infiltration. Additionally, we found that microglia could interact with the tumor microenvironment and genomic features of gliomas, making microglia abundance negatively associated with the prognosis of glioma patients. Microglia abundance was positively correlated with immune genes expression and immune-related pathways. By applying our LASSO Cox regression model to gliomas, we found that patients with high-risk scores had significantly shorter overall survival (OS) than those with low-risk scores. Conclusions: Taken together, our findings suggest that microglia abundance may be negatively associated with survival in gliomas. Based on the novel microglia abundance signatures, we developed a high accuracy LASSO Cox regression model. In this study, we demonstrated that the model accurately predicted the prognosis of glioma patients and could offer new therapeutic targets for microglial-directed therapies. Keywords: Gliomas; Microglia abundance; LASSO Cox regression; TCGA; Signature.- 1 - Citation Format: Chongming Jiang, Evelien Schaafsma, Yanding Zhao, Thinh Nguyen, Kenneth Zhu, Chao Cheng. A microglia associated gene signature predicts survival risk in glioma patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr LB528.
Abstract 2854: Logic gates controlled by priming receptors increase specificity and potency of CAR T cells
Authors: Jasper Williams, Kevin Martinez, Angela Boroughs, Laura Lim, Marian Sandoval, Cate Sue, Matthew Drever, Anzhi Yao, Joseph Choe, Maxim Sidorov, Sophia Phillips, Dina Polyak, Suchismita Mohanty, Stephen Santoro, Aaron Cooper, W. Nicholas Haining
Journal: Cancer Research (2022)

Abstract CAR T cell therapies for solid tumors are limited by a paucity of tumor-specific single target antigens and insufficient potency due to limitations of CAR T biology. Logic gated (LG) CARs increase control of cell therapy activation and target cell killing by requiring recognition of two or more antigens through AND or AND-NOT Boolean logic. They represent an attractive strategy for cell therapy to improve the therapeutic index by increasing specificity for tumor antigens. We created an AND logic gate cassette deliverable by CRISPR-mediated, non-viral, site-specific integration into human T cells. This logic gate activates expression of a MSLN-targeting CAR upon ALPP/G binding of a priming receptor (PrimeR) within high-grade serous carcinoma ovarian tumors. The PrimeR triggers proteolytic release of a chimeric, fully human transcription factor, which then translocates to the nucleus to induce expression of a minigene encoding a CAR. The PrimeR is built only from human protein sequences, reducing theoretical risk of cell therapy immunogenicity and rejection within a patient. In order to test the specificity of our LG CARs, we integrated LG cassettes into a defined site in the T cell genome, and then co-cultured T cells with K562 cells engineered with only one target antigen (K562-ALPG or K562-MSLN), both target antigens (K562-ALPG/MSLN), or neither target antigen (K562). LG CAR T cells only killed K562-ALPG/MSLN cells. The specificity of this LG was also demonstrated in vivo in a dual-flank K562 model, in which only the ALPG/MSLN tumor was inhibited by LG CAR T cells. CAR expression was not observed on LG CAR T cells recovered outside the ALPG/MSLN tumor, and no growth inhibition was observed in K562-MSLN tumors, unlike a constitutive CAR T control. To model priming antigen heterogeneity expected in tumors, we mixed K562-MSLN cells with varying proportions of K562-ALPG/MSLN cells. We found that the presence of only 5-15% ALPG/MSLN cells was sufficient to effect killing of all target cells by the induced MSLN CAR. The ALPG/MSLN LG CAR will be tested as a component of AB-1015, a novel therapy for indications including ovarian, fallopian tube, or primary peritoneal cancer. Citation Format: Jasper Williams, Kevin Martinez, Angela Boroughs, Laura Lim, Marian Sandoval, Cate Sue, Matthew Drever, Anzhi Yao, Joseph Choe, Maxim Sidorov, Sophia Phillips, Dina Polyak, Suchismita Mohanty, Stephen Santoro, Aaron Cooper, W. Nicholas Haining. Logic gates controlled by priming receptors increase specificity and potency of CAR T cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2854.
Biomarkers for the prediction of heart failure and cardiovascular events in patients with type 2 diabetes: a position statement from the Heart Failure Association of the European Society of Cardiology
Authors: Peter Seferović, Dimitrios Farmakis, Antoni Bayes‐Genis, Tuvia Ben Gal, Michael Böhm, Ovidiu Chioncel, Roberto Ferrari, Gerasimos Filippatos, Loreena Hill, Ewa Jankowska, Mitja Lainscak, Yuri Lopatin, Lars H. Lund, Alexandre Mebazaa, Marco Metra, Brenda Moura, Giuseppe Rosano, Thomas Thum, Adriaan Voors, Andrew J.S. Coats
Journal: European Journal of Heart Failure (2022)
Abstract 6077: Mammalian adipose has many tumor features, which suggests the possible way of its evolutionary origin
Authors: Andrei P. Kozlov
Journal: Cancer Research (2022)

Abstract Adipose expansion during obesity has remarkable similarities with the growth of solid tumors. These similarities are the following: the capability to unlimited expansion; reversible plasticity; induction of angiogenesis; chronic inflammation; remodeling and disfunction; systemic influence on the organism; hormone production; production of miRNAs that influence other tissues; immunosuppression; DNA damage and resistance to apoptosis; infiltration in other organs and tissues. The existing similarities between adipose and tumors suggest the possible evolutionary origin of mammalian adipose from some ancestral benign mesenchymal hereditary tumors. Transgenic inducible zebrafish tumor model was used to verify the above hypothesis. We described several genes, which originated in fish and were expressed in fish tumors. Their human orthologs LEP, SPRY1, PPARG, ID2, and CIDEA acquired functions connected with human adipose. They are also involved in tumor development in humans. If the hypothesis of the evolutionary origin of mammalian adipose from the ancestral benign hereditary tumors is correct, it may open new opportunities to resolve the oncological problem and the problem of the obesity epidemic. New interventions targeting LEP, SPRY1, PPARG, ID2, and CIDEA gene network, in addition to what already is going on, can be designed for treatment and prevention of both obesity and tumors. Citation Format: Andrei P. Kozlov. Mammalian adipose has many tumor features, which suggests the possible way of its evolutionary origin [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6077.
Calcium-dependent cytosolic phospholipase A2 activation is implicated in neuroinflammation and oxidative stress associated with ApoE4
Authors: Shaowei Wang, Boyang Li, Victoria Solomon, Alfred Fonteh, Stanley I. Rapoport, David A. Bennett, Zoe Arvanitakis, Helena C. Chui, Patrick M. Sullivan, Hussein N. Yassine
Journal: Molecular Neurodegeneration (2022)

Abstract Background Apolipoprotein E4 ( APOE4 ) is associated with a greater response to neuroinflammation and the risk of developing late-onset Alzheimer’s disease (AD), but the mechanisms for this association are not clear. The activation of calcium-dependent cytosolic phospholipase A 2 (cPLA2) is involved in inflammatory signaling and is elevated within the plaques of AD brains. The relation between APOE4 genotype and cPLA2 activity is not known. Methods Mouse primary astrocytes, mouse and human brain samples differing by APOE genotypes were collected for measuring cPLA2 expression, phosphorylation, and activity in relation to measures of inflammation and oxidative stress. Results Greater cPLA2 phosphorylation, cPLA2 activity and leukotriene B4 (LTB4) levels were identified in ApoE4 compared to ApoE3 in primary astrocytes, brains of ApoE-targeted replacement (ApoE-TR) mice, and in human brain homogenates from the inferior frontal cortex of persons with AD dementia carrying APOE3/4 compared to APOE3/3 . Higher phosphorylated p38 MAPK but not ERK1/2 was found in ApoE4 primary astrocytes and mouse brains than that in ApoE3. Greater cPLA2 translocation to cytosol was observed in human postmortem frontal cortical synaptosomes with recombinant ApoE4 than ApoE3 ex vivo. In ApoE4 astrocytes, the greater levels of LTB4, reactive oxygen species (ROS), and inducible nitric oxide synthase (iNOS) were reduced after cPLA2 inhibition. Conclusions Our findings implicate greater activation of cPLA2 signaling system with APOE4 , which could represent a potential drug target for mitigating the increased neuroinflammation with APOE4 and AD.
Artificial Intelligence and Machine Learning for Lead-to-Candidate Decision-Making and Beyond
Authors: Douglas McNair
Journal: The Annual Review of Pharmacology and Toxicology (2022)

The use of artificial intelligence (AI) and machine learning (ML) in pharmaceutical research and development has to date focused on research: target identification; docking-, fragment-, and motif-based generation of compound libraries; modeling of synthesis feasibility; rank-ordering likely hits according to structural and chemometric similarity to compounds having known activity and affinity to the target(s); optimizing a smaller library for synthesis and high-throughput screening; and combining evidence from screening to support hit-to-lead decisions. Applying AI/ML methods to lead optimization and lead-to-candidate (L2C) decision-making has shown slower progress, especially regarding predicting absorption, distribution, metabolism, excretion, and toxicology properties. The present review surveys reasons why this is so, reports progress that has occurred in recent years, and summarizes some of the issues that remain. Effective AI/ML tools to derisk L2C and later phases of development are important to accelerate the pharmaceutical development process, ameliorate escalating development costs, and achieve greater success rates.
Abstract 3192: EBV-products containing exosomes remodel NPC tumor microenvironment by activating fibroblasts
Authors: Po-Ju Lee, Yun-Hua Sui, Chen-Han Huang, Tzu-Tung Liu, Ngan-Ming Tsang, Shu-Chen Liu
Journal: Cancer Research (2022)

Abstract Epstein-Barr virus (EBV) infection is intimately associated with type III nasopharyngeal carcinoma (NPC). Most NPCs respond well to chemoradiation. Nevertheless, approximately 20% of patients experience recurrence and distant metastasis. Tumor desmoplastic responses and high densities of cancer-associated fibroblasts (CAFs) within tumors have been correlated with poorer prognosis. In this study, we demonstrate that EBV activates fibroblasts via exosomes to remodel a pro-tumoral microenvironment. Exosomes derived from NPC cells contained a high level of fibroblast activation protein alpha (FAPα) and EBV-encoded latent membrane protein 1 (LMP1). Treating primary fibroblasts with these exosomes induced functional changes resembling CAFs. Transcriptomic analysis on exosome-treated fibroblasts revealed genes involved in fibrosis-associated pathways were enriched. Noticeably, treating with EBV products-containing exosomes in fibroblasts enhanced the production of several immune-suppressive cytokines, including IL6, IL8, and MCP-1. Moreover, stimulation with these exosomes enhanced activation of YAP1 signaling, a key pathway linking to fibrosis. The in vivo mouse xenografted NPC studies showed that EBV products-containing exosomes markedly enhanced the severity of tissue fibrosis and tumor growth. IHC analysis on mouse NPC xenografts and human NPC biopsies showed a positive correlation between levels of nuclear YAP1 and FAPα, which were further correlated with an enhanced fibrotic response within tumors. Pharmaceutical intervention with YAP1 inhibitors blocked the exosome-mediated effects on fibroblasts. Collectively, our data suggest that EBV products-containing exosome is a causal factor in CAF formation, which constitutes a pro-tumoral microenvironment to benefit the survival of both tumor and virus itself. Citation Format: Po-Ju Lee, Yun-Hua Sui, Chen-Han Huang, Tzu-Tung Liu, Ngan-Ming Tsang, Shu-Chen Liu. EBV-products containing exosomes remodel NPC tumor microenvironment by activating fibroblasts [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3192.
Abstract 2968: Interrogating the function of histone methyltransferases in MYC-driven medulloblastoma
Authors: Audrey L. Mercier, Jennifer L. Stripay, Silvija Bilokapic, Justin Williams, Stephanie Nance, Jingjing Liu, Steven Philips, Suresh Kandikonda, Marie Morfouace, Aude Bramoulle, Tamara Advedissian, Jiyang Yu, Junmin Peng, Aseem Ansari, Mario Halic, Adam Durbin, Christopher Vakoc, Martine F. Roussel
Journal: Cancer Research (2022)

Abstract Medulloblastoma (MB) is the most common malignant pediatric brain tumor of the cerebellum, with four distinct molecular subgroups, each carrying different clinical prognoses. Group 3 (G3) is the most aggressive subgroup and is associated with amplifications of the MYC gene. MYC expression and function are controlled in part by epigenetic regulation, and interestingly, the few mutations that are found in G3 medulloblastoma are mostly located in genes encoding epigenetic regulators. Surprisingly, many tumors had no mutations raising the question as to whether non-mutated or non-amplified epigenetic regulators may be drivers of G3MB tumorigenesis. We previously found that dysregulation of the H3K27 methyltransferase EZH2 cooperates with MYC in G3MB, indicating that epigenetic regulators may provide a source of potential therapeutic targets. Therefore, to identify novel epigenetic drivers in G3MB, we performed an unbiased shRNA screen of 243 known chromatin regulators. The most intriguing candidate was SMYD3, a multidomain-containing protein with histone H4-lysine 5 (H4K5) methyltransferase activity. Knockdown of SMYD3 suppressed G3MB proliferation in vitro and tumor progression in vivo. SMYD3 protein is nuclear and associated with the MYC promoter. Deletion of SMYD3 results in loss of MYC, G2/M and epithelial-to-mesenchymal target gene expression. Using a multi-omics approach including CUT&amp;RUN sequencing, RNA-seq, DNA methylation, cryo-electron microscopy (cryo-EM) and proteomics we aim to elucidate how SMYD3 controls G3MB tumorigenesis. These results highlight the role of a potentially targetable new epigenetic regulator of tumorigenesis in G3MB. Citation Format: Audrey L. Mercier, Jennifer L. Stripay, Silvija Bilokapic, Justin Williams, Stephanie Nance, Jingjing Liu, Steven Philips, Suresh Kandikonda, Marie Morfouace, Aude Bramoulle, Tamara Advedissian, Jiyang Yu, Junmin Peng, Aseem Ansari, Mario Halic, Adam Durbin, Christopher Vakoc, Martine F. Roussel. Interrogating the function of histone methyltransferases in MYC-driven medulloblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2968.
Interpenetrating Polymer Network Hydrogels Formed Using Antibiotics as a Dynamic Crosslinker for Treatment of Infected Wounds
Authors: Mengjing Fu, Yingying Gan, Fenglin Jiang, Xue Lv, Nathanael Tan, Xiaomiao Zhao, Yi Yan Yang, Peiyan Yuan, Xin Ding
Journal: Advanced Healthcare Materials (2022)

Abstract Antibacterial hydrogels, particularly antibiotic‐loaded hydrogels, are promising wound dressing materials for treatment of bacteria‐infected wound. However, it is challenging to achieve sustained release of antibiotics from hydrogels through physical encapsulation of the antibiotics. Herein, an interpenetrating polymer network P(AA‐ co ‐HEMA) Gen hydrogel is reported with double crosslinking formed by free radical polymerization of 2‐hydroxyethyl methacrylate (HEMA) and acrylic acid (AA), while using the antibiotic gentamicin (Gen) as the dynamic physical crosslinker. Gentamicin is incorporated into the hydrogel networks via electrostatic interaction between the carboxyl groups of poly(acrylic acid) and the amino groups of gentamicin, which leads to pH‐responsive drug release and a significant increase in mechanical strength (i.e., elastic modulus, viscous modulus, and compressive modulus). More importantly, the hydrogels with optimal compositions demonstrate long‐lasting antibacterial activity against both Gram‐positive bacteria ( Staphylococcus aureus ) and Gram‐negative bacteria ( Escherichia coli ) over 28 d. The in vivo studies that are conducted in an S. aureus ‐infected full‐thickness skin wound model demonstrate that the double crosslinking hydrogels loaded with gentamicin eliminate bacteria in the wounds more effectively and significantly accelerate wound healing as compared to 3M dressing and the control without any treatment. Taken together, this antibiotic‐loaded interpenetrating polymer network hydrogel is potentially a promising wound dressing material for the treatment of bacteria‐infected wound.
Probiotic‐derived nanoparticles inhibit ALD through intestinal miR194 suppression and subsequent FXR activation
Authors: Mengwei Jiang, Fengyuan Li, Yunhuan Liu, Zelin Gu, Lihua Zhang, Jiyeon Lee, Liqing He, Vatsalya Vatsalya, Huang‐Ge Zhang, Zhongbin Deng, Xiang Zhang, Shao‐Yu Chen, Grace L. Guo, Shirish Barve, Craig J. McClain, Wenke Feng
Journal: Hepatology (2022)

Background and Aims: Intestinal farnesoid X receptor (FXR) plays a critical role in alcohol‐associated liver disease (ALD). We aimed to investigate whether alcohol‐induced dysbiosis increased intestinal microRNA194 (miR194) that suppressed Fxr transcription and whether Lactobacillus rhamnosus GG–derived exosome‐like nanoparticles (LDNPs) protected against ALD through regulation of intestinal miR194‐FXR signaling in mice. Approach and Results: Binge‐on‐chronic alcohol exposure mouse model was utilized. In addition to the decreased ligand‐mediated FXR activation, alcohol feeding repressed intestinal Fxr transcription and increased miR194 expression. This transcriptional suppression of Fxr by miR194 was confirmed in intestinal epithelial Caco‐2 cells and mouse enteriods. The alcohol feeding–reduced intestinal FXR activation was further demonstrated by the reduced FXR reporter activity in fecal samples and by the decreased fibroblast growth factor 15 (Fgf15) messenger RNA (mRNA) in intestine and protein levels in the serum, which caused an increased hepatic bile acid synthesis and lipogeneses. We further demonstrated that alcohol feeding increased‐miR194 expression was mediated by taurine‐upregulated gene 1 (Tug1) through gut microbiota regulation of taurine metabolism. Importantly, 3‐day oral administration of LDNPs increased bile salt hydrolase (BSH)‐harboring bacteria that decreased conjugated bile acids and increased gut taurine concentration, which upregulated Tug1, leading to a suppression of intestinal miR194 expression and recovery of FXR activation. Activated FXR upregulated FGF15 signaling and subsequently reduced hepatic bile acid synthesis and lipogenesis and attenuated ALD. These protective effects of LDNPs were eliminated in intestinal Fxr ΔIEC and Fgf15 −/− mice. We further showed that miR194 was upregulated, whereas BSH activity and taurine levels were decreased in fecal samples of patients with ALD. Conclusions: Our results demonstrated that gut microbiota–mediated miR194 regulation contributes to ALD pathogenesis and to the protective effects of LDNPs through modulating intestinal FXR signaling.
Abstract 3825: Germline modifiers of the tumor immune microenvironment reveal drivers of immunotherapy response
Authors: Meghana Pagadala, Victoria Wu, Eva Pérez-Guijarro, Hyo Kim, Andrea Castro, James Talwar, Cristian Gonzalez-Colin, Steven Cao, Benjamin J. Schmiedel, Timothy Sears, Shervin Goudarzi, Divya Kirani, Rany M. Salem, Gerald P. Morris, Olivier Harismendy, Sandip P. Patel, Jill P. Mesirov, Maurizio Zanetti, Chi-Ping Day, Chun C. Fan, Wesley K. Thompson, Glenn Merlino, J. Silvio Gutkind, Pandurangan Vijayanand, Hannah Carter
Journal: Cancer Research (2022)

Abstract With the continued promise of immunotherapy as an avenue for treating cancer, understanding how host genetics contributes to the tumor immune microenvironment (TIME) is essential to tailoring cancer risk screening and treatment strategies. Using genotypes from over 8,000 European individuals in The Cancer Genome Atlas and 137 heritable tumor immune phenotype components (IP components), we identified and investigated 532 TIME-SNPs. Focusing on 77 variants that were relevant to cancer risk, survival, or treatment response, we explored their potential to reveal novel targets for immunotherapy. Many variants overlapped regions with histone marks indicating active transcription, and influenced gene activities in specific immune cell subsets, such as macrophages and dendritic cells. TIME-SNPs implicated genes such as LAIR1, TREX1, CTSS, CTSW and LILRB2 were differentially expressed between responders and non-responders to immune-checkpoint blockade (ICB) in preclinical studies. Of these, LILRB2 and LAIR1 have already been identified as putative targets for immunotherapy. Here we found that inhibition of CTSS led to better tumor control and survival in murine models, alone or in combination with anti-PD-1. Collectively we show that through an integrative approach, it is possible to link host genetics to TIME characteristics, informing novel biomarkers for cancer risk and target identification in immunotherapy. Citation Format: Meghana Pagadala, Victoria Wu, Eva Pérez-Guijarro, Hyo Kim, Andrea Castro, James Talwar, Cristian Gonzalez-Colin, Steven Cao, Benjamin J. Schmiedel, Timothy Sears, Shervin Goudarzi, Divya Kirani, Rany M. Salem, Gerald P. Morris, Olivier Harismendy, Sandip P. Patel, Jill P. Mesirov, Maurizio Zanetti, Chi-Ping Day, Chun C. Fan, Wesley K. Thompson, Glenn Merlino, J. Silvio Gutkind, Pandurangan Vijayanand, Hannah Carter. Germline modifiers of the tumor immune microenvironment reveal drivers of immunotherapy response [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3825.